I had that problem too! I just use the touch up paint from Mopar to match the color.
And, don't tell Infernogirl, but, I finally had to go with the Mopar mud flaps!!!
They do fit with step bars! I didn't think they would but it worked with mine.
Also, they work with the Rock Rails as well!
I also have changed the screws and have small tools handy so I can pull them off quickly for off-road, etc.
Works well for me if you can stand the look!